BioC 3.1: CHECK report for sigaR on petty

Package: sigaR

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.12.0.tar.gz

StartedAt: 2015-10-09 01:58:54 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:04:45 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 351.1 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/sigaR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sigaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigaR’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sigaR’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘penalized’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
summary,entTest : .local: warning in round(object@statistic, d = 3):
  partial argument match of 'd' to 'digits'
summary,entTest : .local: warning in round(object@p.value, d = 3):
  partial argument match of 'd' to 'digits'
summary,miTest : .local: warning in round(object@statistic, d = 3):
  partial argument match of 'd' to 'digits'
summary,miTest : .local: warning in round(object@p.value, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@betas, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@tau2s, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@av.sigma2s, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@rho, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@shrinkage, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@loglik, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@betas, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@tau2s, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@av.sigma2s, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@rho, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@shrinkage, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@loglik, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@statistic, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@p.value, d = 3):
  partial argument match of 'd' to 'digits'
.pi0est: no visible global function definition for ‘convest’
cghCall2maximumSubset: no visible binding for global variable ‘sigaR’
cghCall2order: no visible global function definition for ‘probdloss’
cghCall2order: no visible global function definition for ‘probdloss<-’
cghCall2subset: no visible global function definition for ‘probdloss’
cghCall2weightedSubset: no visible global function definition for
  ‘probdloss’
cghCall2weightedSubset: no visible binding for global variable ‘sigaR’
cghSeg2weightedSubset: no visible binding for global variable ‘sigaR’
entropyTest: no visible binding for global variable ‘sigaR’
entropyTest: no visible binding for global variable ‘corpcor’
ExpressionSet2weightedSubset: no visible binding for global variable
  ‘sigaR’
matchAnn2Ann: no visible binding for global variable ‘sigaR’
matchCGHcall2ExpressionSet: no visible binding for global variable
  ‘sigaR’
merge2cghCalls: no visible global function definition for ‘probdloss’
mutInfTest: no visible binding for global variable ‘sigaR’
mutInfTest: no visible binding for global variable ‘corpcor’
RCMestimation : RCMmlH2: multiple local function definitions for
  ‘tau.estimator’ with different formal arguments
RCMtest: no visible binding for global variable ‘sigaR’
RCMtest: no visible binding for global variable ‘quadprog’
RCMtest: no visible binding for global variable ‘MASS’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [248s/248s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     181.837 13.128 195.273
cisEffectTune   25.146  0.225  25.401
pathway2sample   4.144  1.215   5.361
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/sigaR.Rcheck/00check.log’
for details.

* installing *source* package ‘sigaR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.711	0.028	1.741
ExpressionSet2order	0.016	0.001	0.017
ExpressionSet2subset	0.011	0.001	0.012
ExpressionSet2weightedSubset	0.260	0.009	0.269
RCMestimation	1.429	0.015	1.447
RCMrandom	1.305	0.002	1.308
RCMtest	4.820	0.004	4.824
cghCall2cghSeg	0.057	0.001	0.057
cghCall2maximumSubset	0.360	0.005	0.365
cghCall2order	0.018	0.001	0.018
cghCall2subset	0.081	0.001	0.083
cghCall2weightedSubset	0.345	0.004	0.348
cghSeg2order	0.078	0.001	0.080
cghSeg2subset	0.143	0.002	0.143
cghSeg2weightedSubset	0.309	0.002	0.311
cisEffectPlot	0.081	0.002	0.084
cisEffectTable	2.695	0.055	2.753
cisEffectTest	2.372	0.061	2.433
cisEffectTune	25.146	0.225	25.401
cisTest-class	0.004	0.001	0.004
entTest-class	0.001	0.000	0.002
entropyTest	0.252	0.007	0.258
expandMatching2singleIDs	0.073	0.002	0.074
getSegFeatures	0.014	0.001	0.015
hdEntropy	0.021	0.001	0.022
hdMI	0.423	0.004	0.429
matchAnn2Ann	0.051	0.002	0.058
matchCGHcall2ExpressionSet	0.073	0.003	0.076
merge2ExpressionSets	0.096	0.001	0.098
merge2cghCalls	0.102	0.001	0.102
miTest-class	0.001	0.001	0.001
mutInfTest	181.837	13.128	195.273
nBreakpoints	0.278	0.005	0.282
pathway1sample	0.164	0.014	0.179
pathway2sample	4.144	1.215	5.361
pathwayFit-class	0.002	0.000	0.002
pathwayPlot	0.164	0.036	0.199
pollackCN16	0.007	0.000	0.009
pollackGE16	0.004	0.000	0.004
profilesPlot	0.217	0.008	0.225
rcmFit-class	0.002	0.000	0.003
rcmTest-class	0.002	0.000	0.002
splitMatchingAtBreakpoints	0.325	0.005	0.329
uniqGenomicInfo	0.012	0.001	0.013